Our initial study examined stool and urine energy losses in obese versus lean individuals on two standard (2400 kcal/d and 3400 kcal/d each given over 3 days) diets. Preliminary results from an initial 14 lean and 9 obese individuals failed to show any difference in stool or urine energy loss. The range of calories stool was large, varying from 2 to 9 % in both groups. Lean individuals absorbed more (had less stool energy loss) on the higher calorie diet compared to obese individuals. Percent changes in the major gut phylotypes, Firimutes and Bacteroidetes, were associated with changes in nutrient load. Percent of Firmicutes increased with nutrient load while Bacteroidetes decreased. In addition, in lean individuals, these changes in the major phylotypes were associated with stool energy loss, such that a 20% increase or decrease in Firmcutes/Bacteroidetes was associated with approximately 150 kcal/day difference in stool energy loss. Based on this preliminary work, we completed a new study to confirm and extend the above findings. In this study, stool energy loss and changes in gut microbiota were measured during over and underfeeding (150 and 50% based on calculated weight maintaining calories). Following this, volunteers were randomized to receive the antibiotic oral vancomycin versus placebo (in a double blind randomized fashion). Oral vancomycin is not absorbed in healthy individuals and will selectively change the gut bacterial population. We found important and previously unreported differences in nutrient absorption changes in response to overfeeding and vancomycin. We have also found important changes in the gut microbiota that support its role in nutrient absorption.